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Experiments were made in order to evaluate the accuracy and sensitivity of a photoacoustic infrared trace gas analyzer (TGA) in conjunction with an automatic opening and closing chamber system developed for near-continuous (2 min intervals) soil gaseous flux measurements. Humidity interference tests on N2O, CH4, and CO2 concentrations measured by the TGA were carried out, and the results showed a linear interference, with correction factors of 3 × 10−5x, 1.9 × 10−3x and 4.4 × 10−3x(x = H2O vapor ppm), respectively. CO2 interference on N2O and CH4 signals were also linear, with average correction factors of 2.8 × 10−4x and 6 × 10−5 x (x = CO2 ppm), respectively. Laboratory intercomparisons between the TGA and GC measurements of N2O and CH4 standards showed good agreement (R2 > 0.993), indicating the accuracy of the TGA for measurement of these gases at concentrations up to 100 and 40 ppm N2O and CH4, respectively. The relatively rapid measurement time for up to five gases simultaneously in 2 min, linearity, and ease of operation of the TGA represent major advantages compared to gas chromatography (GC). The automated chamber system provides a continuous measurement of fluxes with minimum disturbance to the soil environment enclosed by the chamber and provides the means, for example, of quantifying diurnal variability. In situ measurements of N2O-N and CH4-C fluxes with a sensitivity <10 g ha−1 d−1 (11.6 ng m−2 s−1), as well as of CO2 and water vapor (H2O), can be measured by the TGA when used with the automated system, and fluxes at background levels (i.e., from unfertilized soils) can be determined.